Despite the phenomenal increase in the identification of genes and gene products of the human genome from the human genome sequencing, major challenges remain in the understanding of regulation and transduction of genetic information. Mounting evidence shows that site-specific post-translational modifications of histones - the main protein component of chromatin - play an important role in controlling of the capacity of the eukaryotic genome to store, release and inherit biological information. Such studies of histone modifications led to the histone code hypothesis, which predicts that "multiple histone modifications, acting in a combinatorial or sequential fashion on one or multiple histone tails, specify unique downstream functions". The models for the sequential readout of the histone code are supported by several findings, including our own discovery that bromodoains function as histone acetyl- lysine binding domains. However, the prediction for combinatorial readout of the histone code currently lacks evidence. In this Project, we aim to develop an integrated structure-guided paradigm in order to define fundamental principles that dictate histone-directed chromatin function. Through systematic characterization of the structure-function relationships of conserved modular domains present in many chromatin and transcription proteins, we aim to test and develop new mechanistic models that constitute sequential and combinatorial readout of the histone code in epigenetic control of gene expression and silencing. To attain this goal, our Specific Aims are: (1) to determine ligand binding selectivity of bromodomains; (2) to define the histone binding activity of the tandem bromodomain and PHD finger modules; and (3) to define combinatorial readout of the histone code by tandem chromatin protein modules. We expect that this new strategy of structure-based functional profiling of the evolutionary conserved protein domains, as being developed and enriched through the planned studies in this Project, may be generalizable to gain new mechanistic understanding of the fundamental and complex cellular functions of domain-bearing proteins and protein complexes in a wide array of cellular processes with far-reaching implications for human biology and disease.